I know we can't change the existing pop-ups for a disease. We can turn them off, but without proper replacements, that seems like a good way to break a scenario (specifically, the three special plagues, which use those events to trigger adversary actions.) However, just being able to look at them would be a tremendous help; one could manually create replacements with the same or similar trigger conditions, but with different images, text, responses, et cetera.

I'm currently trying to make edits to a shadow plague scenario. While I can easily figure out what triggers some pop-ups (mostly the ones related to symptoms), the ones controlling Templar awareness or activity - I can only guess their parameters, and the awareness/combat strength numbers involved would just be a game of trial and error. Given you can't load a saved game after altering the scenario, the only way to test whether a change worked is to start a new game and play up to the point where you hope something will trigger, and that gets... tedious.